[Mristudio-users] automate DTIstudio processing

[Youngmin Huh]

I edited map file generated by ROIEditor as below.
There are two ROIs with 'or(0)' operation for the first one, and
'and(1)' operation for the second one.
-----------------------------------------------------
*** ROI Map ***

Begin
	ImageWidth:	240
	ImageHeight:	240
	ImageSlices:	152

	PixelSizeWidth:	1.000000
	PixelSizeHeight:	1.000000
	SliceThickness:	1.000000

	SliceOrientation:	1
	SliceSequencing:	0

	BinaryFile:	E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_L_b.dat
	Operation:	0

	BinaryFile:	E:\data\isotropic_data\ADHD\72804182\DTIstudio\test_AAL\ROImask\Amygdala_R_b.dat
	Operation:	1

End

Note:
	Slice Orientation: 0=Coronal, 1=Axial, 2=Sagittal
	Slice Sequencing:  0=Positive, 1=Negative
	ROI Operation:  0=OR, 1=AND, 3=NOT

*** ROI Map ***
-----------------------------------------------------

And I load map file as Binary map format on DTI studio, but nothing happened.
I can load the map file on ROIEditor, but can't load at DTI studio. I
wonder why.

Thanks,

YM Huh


2013/8/7 susumu mori <smoriw at gmail.com>:
> Hi YM,
>
> Did you open the ROI files as BinaryMap format?
> Once you save BinaryMap by RoiEditor, you have to edit the saved text file
> and specify how you want to combine the multiple ROI files using AND/OR/NOT
> operations.
>
>
> On Tue, Aug 6, 2013 at 10:29 PM, Youngmin Huh <ymin1123 at gmail.com> wrote:
>>
>> Thanks for your comment!
>> I'm using ROIs for fiber tracking.
>>
>> I used ROIeditor to generate binay map files, and changed
>> ROIMap_map.dat to ROIMap_map.map.
>> It worked! I can load multiple RoIs at ROIEditor, but I can't figure
>> out how I could load it on DTI studio.
>> I tried to load map file using the "load" icon in "Fiber" tab,
>> "ROI-Operation" section, but nothing happened.
>> Of course I finished whole brain fiber tracking before I load ROIs.
>> How could I find fibers connecting ROIs with my map file on DTI studio?
>>
>> Thanks,
>>
>> YM Huh
>>
>> 2013/8/7 susumu mori <smoriw at gmail.com>:
>> > Are you using ROIs for image quantification or fiber tracking?
>> > From the second question, I guess you want to do a comprehensive fiber
>> > tracking with a lot of ROIs.
>> > If that is the case, Yajing is the right person to ask.
>> > We do have command line-version of the tracking.
>> >
>> > Also, please take a look at RoiEditor at www.mristudio.org. It manages
>> > multiple ROIs much better.
>> > You can find some tips in the FAQ section.
>> >
>> >
>> > On Tue, Aug 6, 2013 at 5:01 AM, Youngmin Huh <ymin1123 at gmail.com> wrote:
>> >>
>> >> Hi, I'm a new user.
>> >> I have been struggling with DTIstudio for few weeks.
>> >> I have some questions to ask.
>> >>
>> >> 1) how can I define multiple ROIs?
>> >> I drew two ROIs with "ROI drawing" on "ROi" tab, and saved them into
>> >> "binary maps".
>> >> But It generated 3 dat files, but no map file (ROIMap_00.dat,
>> >> ROIMap_01.dat, ROIMap_map.dat).
>> >> I tried again with ROI editor, but It didn't work either. It generated
>> >> only dat files.
>> >> How can I generate .map file to load ROIs?
>> >>
>> >> 2) Is there any way to automate DTI processing?
>> >> I'm going to use 116 ROI masks to obtain whole brain connectivity.
>> >> It seems like hard work to do all this process manually.
>> >>
>> >> Any comment would be appreciate.
>> >>
>> >> Thanks,
>> >>
>> >> YM Huh
>> >> _______________________________________________
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>> >
>> >
>> >
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